Schematic overview of the cellular and molecular mechanisms involved in the cancer progression, including the proposed cellular and molecular mechanisms in cancer cells trajectory. AT1: alveolar type 1 cells; AT2: alveolar type 2 cells; AAH: atypical adenomatous hyperplasia; AIS: adenocarcinoma in situ; MIA: minimally invasive adenocarcinoma; IA: invasive adenocarcinoma; EMT: epithelial-mesenchymal transition

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	Gene summary
	Malignant transformation analysis
	Malignant transformation related pathway analysis
	Cell-cell communication analysis
	Single-cell gene regulatory network inference analysis
	Somatic mutation of malignant transformation related genes
	Related drugs of malignant transformation related genes

Gene: RPS7

Gene summary for RPS7

Gene summary.

Gene information	Species	Human
	Gene symbol	RPS7
	Gene ID	6201
	Gene name	ribosomal protein S7
	Gene Alias	DBA8
	Cytomap	2p25.3
	Gene Type	protein-coding
	GO ID	GO:0001838
	UniProtAcc	P62081

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Malignant transformation analysis

Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells

Malignant transformation involving gene list.

Entrez ID	Symbol	Replicates	Species	Organ	Tissue	Adj P-value	Log2FC	Malignancy
6201	RPS7	GSM4909281	Human	Breast	IDC	2.90e-39	-3.15e-01	0.21
6201	RPS7	GSM4909285	Human	Breast	IDC	2.10e-54	2.78e-01	0.21
6201	RPS7	GSM4909286	Human	Breast	IDC	7.60e-12	1.32e-01	0.1081
6201	RPS7	GSM4909293	Human	Breast	IDC	1.72e-23	-1.65e-01	0.1581
6201	RPS7	GSM4909295	Human	Breast	IDC	1.57e-08	-3.45e-01	0.0898
6201	RPS7	GSM4909297	Human	Breast	IDC	8.13e-09	-2.12e-01	0.1517
6201	RPS7	GSM4909298	Human	Breast	IDC	9.85e-21	-1.75e-01	0.1551
6201	RPS7	GSM4909299	Human	Breast	IDC	8.19e-09	-1.21e-01	0.035
6201	RPS7	GSM4909301	Human	Breast	IDC	1.41e-24	-2.40e-01	0.1577
6201	RPS7	GSM4909302	Human	Breast	IDC	8.81e-27	-4.05e-01	0.1545
6201	RPS7	GSM4909304	Human	Breast	IDC	5.75e-12	-1.39e-01	0.1636
6201	RPS7	GSM4909306	Human	Breast	IDC	7.62e-17	-1.87e-01	0.1564
6201	RPS7	GSM4909307	Human	Breast	IDC	2.12e-07	-1.39e-01	0.1569
6201	RPS7	GSM4909308	Human	Breast	IDC	3.86e-14	-2.02e-01	0.158
6201	RPS7	GSM4909309	Human	Breast	IDC	2.60e-02	-2.11e-01	0.0483
6201	RPS7	GSM4909311	Human	Breast	IDC	4.91e-27	-4.53e-01	0.1534
6201	RPS7	GSM4909312	Human	Breast	IDC	1.82e-06	-1.61e-01	0.1552
6201	RPS7	GSM4909313	Human	Breast	IDC	3.66e-08	-2.69e-01	0.0391
6201	RPS7	GSM4909315	Human	Breast	IDC	1.89e-14	-2.47e-01	0.21
6201	RPS7	GSM4909316	Human	Breast	IDC	1.61e-04	-3.66e-01	0.21

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Transcriptomic changes along malignancy continuum.

Tissue	Expression Dynamics	Abbreviation
Breast		IDC: Invasive ductal carcinoma
		DCIS: Ductal carcinoma in situ
		Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers
Cervix		CC: Cervix cancer
		HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions
		N_HPV: HPV-infected normal cervix
Colorectum (GSE201348)		FAP: Familial adenomatous polyposis
		CRC: Colorectal cancer
Colorectum (HTA11)		AD: Adenomas
		SER: Sessile serrated lesions
		MSI-H: Microsatellite-high colorectal cancer
		MSS: Microsatellite stable colorectal cancer
Endometrium		AEH: Atypical endometrial hyperplasia
		EEC: Endometrioid Cancer
Esophagus		ESCC: Esophageal squamous cell carcinoma
		HGIN: High-grade intraepithelial neoplasias
		LGIN: Low-grade intraepithelial neoplasias
Liver		HCC: Hepatocellular carcinoma
		NAFLD: Non-alcoholic fatty liver disease
Lung		AAH: Atypical adenomatous hyperplasia
		AIS: Adenocarcinoma in situ
		IAC: Invasive lung adenocarcinoma
		MIA: Minimally invasive adenocarcinoma
Oral Cavity		EOLP: Erosive Oral lichen planus
		LP: leukoplakia
		NEOLP: Non-erosive oral lichen planus
		OSCC: Oral squamous cell carcinoma
Prostate		BPH: Benign Prostatic Hyperplasia
Skin		AK: Actinic keratosis
		cSCC: Cutaneous squamous cell carcinoma
		SCCIS:squamous cell carcinoma in situ
Thyroid		ATC: Anaplastic thyroid cancer
		HT: Hashimoto's thyroiditis
		PTC: Papillary thyroid cancer

∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage.

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Malignant transformation related pathway analysis

Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer

Figure of enriched GO biological processes.

Tissue	Disease Stage	Enriched GO biological Processes
Colorectum	AD
Colorectum	SER
Colorectum	MSS
Colorectum	MSI-H
Colorectum	FAP

∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust).

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Enriched GO biological processes.

GO ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	Count
GO:0060606	Colorectum	AD	tube closure	30/3918	89/18723	3.42e-03	2.49e-02	30
GO:0035148	Colorectum	AD	tube formation	45/3918	148/18723	4.13e-03	2.87e-02	45
GO:0001838	Colorectum	AD	embryonic epithelial tube formation	38/3918	121/18723	4.40e-03	3.01e-02	38
GO:1904667	Colorectum	AD	negative regulation of ubiquitin protein ligase activity	7/3918	12/18723	5.09e-03	3.38e-02	7
GO:0042274	Colorectum	AD	ribosomal small subunit biogenesis	25/3918	73/18723	5.69e-03	3.64e-02	25
GO:0072175	Colorectum	AD	epithelial tube formation	40/3918	132/18723	6.98e-03	4.29e-02	40
GO:0021915	Colorectum	AD	neural tube development	45/3918	152/18723	7.05e-03	4.31e-02	45
GO:00021811	Colorectum	SER	cytoplasmic translation	102/2897	148/18723	1.38e-48	8.49e-45	102
GO:00421761	Colorectum	SER	regulation of protein catabolic process	126/2897	391/18723	5.33e-17	2.52e-14	126
GO:19033621	Colorectum	SER	regulation of cellular protein catabolic process	91/2897	255/18723	1.22e-15	5.36e-13	91
GO:19030501	Colorectum	SER	regulation of proteolysis involved in cellular protein catabolic process	77/2897	221/18723	7.85e-13	2.00e-10	77
GO:20012421	Colorectum	SER	regulation of intrinsic apoptotic signaling pathway	59/2897	164/18723	8.42e-11	1.20e-08	59
GO:00971931	Colorectum	SER	intrinsic apoptotic signaling pathway	87/2897	288/18723	1.67e-10	2.32e-08	87
GO:20012331	Colorectum	SER	regulation of apoptotic signaling pathway	101/2897	356/18723	3.05e-10	4.07e-08	101
GO:20000581	Colorectum	SER	regulation of ubiquitin-dependent protein catabolic process	57/2897	164/18723	7.98e-10	8.74e-08	57
GO:00316471	Colorectum	SER	regulation of protein stability	86/2897	298/18723	2.56e-09	2.42e-07	86
GO:19033201	Colorectum	SER	regulation of protein modification by small protein conjugation or removal	70/2897	242/18723	6.84e-08	4.42e-06	70
GO:00508211	Colorectum	SER	protein stabilization	58/2897	191/18723	1.46e-07	8.59e-06	58
GO:00313961	Colorectum	SER	regulation of protein ubiquitination	62/2897	210/18723	1.69e-07	9.71e-06	62
GO:00098951	Colorectum	SER	negative regulation of catabolic process	84/2897	320/18723	3.93e-07	2.06e-05	84

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Enriched KEGG pathways.

Pathway ID	Tissue	Disease Stage	Description	Gene Ratio	Bg Ratio	pvalue	p.adjust	qvalue	Count
hsa0301018	Breast	Precancer	Ribosome	80/684	167/8465	7.33e-44	2.32e-41	1.77e-41	80
hsa0517118	Breast	Precancer	Coronavirus disease - COVID-19	81/684	232/8465	3.74e-32	2.36e-30	1.81e-30	81
hsa0301019	Breast	Precancer	Ribosome	80/684	167/8465	7.33e-44	2.32e-41	1.77e-41	80
hsa0517119	Breast	Precancer	Coronavirus disease - COVID-19	81/684	232/8465	3.74e-32	2.36e-30	1.81e-30	81
hsa0301024	Breast	IDC	Ribosome	83/867	167/8465	6.07e-39	9.87e-37	7.38e-37	83
hsa0517124	Breast	IDC	Coronavirus disease - COVID-19	86/867	232/8465	1.50e-28	9.72e-27	7.27e-27	86
hsa0301034	Breast	IDC	Ribosome	83/867	167/8465	6.07e-39	9.87e-37	7.38e-37	83
hsa0517134	Breast	IDC	Coronavirus disease - COVID-19	86/867	232/8465	1.50e-28	9.72e-27	7.27e-27	86
hsa0301044	Breast	DCIS	Ribosome	82/846	167/8465	8.69e-39	1.40e-36	1.03e-36	82
hsa0517144	Breast	DCIS	Coronavirus disease - COVID-19	86/846	232/8465	2.42e-29	1.56e-27	1.15e-27	86
hsa0301054	Breast	DCIS	Ribosome	82/846	167/8465	8.69e-39	1.40e-36	1.03e-36	82
hsa0517154	Breast	DCIS	Coronavirus disease - COVID-19	86/846	232/8465	2.42e-29	1.56e-27	1.15e-27	86
hsa0517120	Cervix	CC	Coronavirus disease - COVID-19	111/1267	232/8465	1.82e-33	5.90e-31	3.49e-31	111
hsa0301020	Cervix	CC	Ribosome	85/1267	167/8465	3.17e-28	5.14e-26	3.04e-26	85
hsa05171110	Cervix	CC	Coronavirus disease - COVID-19	111/1267	232/8465	1.82e-33	5.90e-31	3.49e-31	111
hsa03010110	Cervix	CC	Ribosome	85/1267	167/8465	3.17e-28	5.14e-26	3.04e-26	85
hsa0301025	Cervix	HSIL_HPV	Ribosome	80/459	167/8465	9.61e-58	2.82e-55	2.28e-55	80
hsa0517125	Cervix	HSIL_HPV	Coronavirus disease - COVID-19	91/459	232/8465	2.14e-56	3.13e-54	2.53e-54	91
hsa0301035	Cervix	HSIL_HPV	Ribosome	80/459	167/8465	9.61e-58	2.82e-55	2.28e-55	80
hsa0517135	Cervix	HSIL_HPV	Coronavirus disease - COVID-19	91/459	232/8465	2.14e-56	3.13e-54	2.53e-54	91

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Cell-cell communication analysis

Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states

Ligand

Receptor

LRpair

Pathway

Tissue

Disease Stage

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Single-cell gene regulatory network inference analysis

Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states

Cell Type

Tissue

Disease Stage

Target Gene

RSS

Regulon Activity

∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression.

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Somatic mutation of malignant transformation related genes

Annotation of somatic variants for genes involved in malignant transformation

Hugo Symbol

Variant Class

Variant Classification

dbSNP RS

HGVSc

HGVSp

HGVSp Short

SWISSPROT

BIOTYPE

SIFT

PolyPhen

Tumor Sample Barcode

Tissue

Histology

Sex

Age

Stage

Therapy Types

Drugs

Outcome

RPS7

SNV

Missense_Mutation

novel

c.241N>T

p.Arg81Cys

p.R81C

P62081

protein_coding

tolerated(0.1)

benign(0.07)

TCGA-D8-A1XJ-01

Breast

breast invasive carcinoma

Female

>=65

III/IV

Hormone Therapy

tamoxiphen

RPS7

SNV

Missense_Mutation

novel

c.91N>C

p.Glu31Gln

p.E31Q

P62081

protein_coding

deleterious(0.04)

possibly_damaging(0.58)

TCGA-EK-A2RB-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Unknown

RPS7

SNV

Missense_Mutation

c.58N>C

p.Glu20Gln

p.E20Q

P62081

protein_coding

deleterious(0.01)

possibly_damaging(0.897)

TCGA-Q1-A73O-01

Cervix

cervical & endocervical cancer

Female

<65

I/II

Chemotherapy

cisplatin

RPS7

SNV

Missense_Mutation

c.347N>A

p.Arg116His

p.R116H

P62081

protein_coding

tolerated(0.1)

benign(0.114)

TCGA-CM-6162-01

Colorectum

colon adenocarcinoma

Female

<65

III/IV

Chemotherapy

oxaliplatin

RPS7

SNV

Missense_Mutation

novel

c.352N>G

p.Arg118Gly

p.R118G

P62081

protein_coding

deleterious(0.01)

probably_damaging(0.939)

TCGA-AJ-A3EK-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Chemotherapy

carboplatin

RPS7

SNV

Missense_Mutation

c.449N>A

p.Gly150Asp

p.G150D

P62081

protein_coding

deleterious(0)

possibly_damaging(0.795)

TCGA-AP-A051-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

RPS7

SNV

Missense_Mutation

novel

c.393G>T

p.Glu131Asp

p.E131D

P62081

protein_coding

tolerated(0.16)

benign(0.026)

TCGA-AP-A059-01

Endometrium

uterine corpus endometrioid carcinoma

Female

>=65

I/II

Unknown

RPS7

SNV

Missense_Mutation

c.412N>A

p.Glu138Lys

p.E138K

P62081

protein_coding

deleterious(0.01)

probably_damaging(0.975)

TCGA-AP-A0LM-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

III/IV

Chemotherapy

cisplatin

RPS7

SNV

Missense_Mutation

novel

c.568N>T

p.Pro190Ser

p.P190S

P62081

protein_coding

deleterious(0.03)

possibly_damaging(0.542)

TCGA-B5-A11E-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

RPS7

SNV

Missense_Mutation

c.117N>T

p.Gln39His

p.Q39H

P62081

protein_coding

deleterious(0.04)

benign(0.049)

TCGA-B5-A11Z-01

Endometrium

uterine corpus endometrioid carcinoma

Female

<65

I/II

Unknown

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Related drugs of malignant transformation related genes

Identification of chemicals and drugs interact with genes involved in malignant transfromation

(DGIdb 4.0)

Entrez ID

Symbol

Category

Interaction Types

Drug Claim Name

Drug Name

PMIDs

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